Read by QxMD icon Read

haplotype analysis

Li-Ling Yue, Fu-Chao Wang, Ming-Long Zhang, Dan Liu, Ping Chen, Qing-Bu Mei, Peng-Hui Li, Hong-Ming Pan, Li-Hong Zheng
We tested the hypothesis that genetic variation in ATM and BMI-1 genes can alter the risk of breast cancer through genotyping 6 variants among 524 breast cancer cases and 518 cancer-free controls of Han nationality. This was an observational, hospital-based, case-control association study. Analyses of single variant, linkage, haplotype, interaction and nomogram were performed. Risk was expressed as odds ratio (OR) and 95% confidence interval (CI). All studied variants were in the Hardy-Weinberg equilibrium and were not linked...
April 24, 2018: Journal of Cellular and Molecular Medicine
Sanjay Singh, Manish Gupta, Rajeev Kumar Seam, Harish Changotra
INTRODUCTION: Altered expression of many E2F family members have been reported in various human cancers. In this study, we investigated the role of non-synonymous single nucleotide polymorphisms (rs3213172 C/T, rs3213173 C/T, and rs3213176 G/A) of the gene E2F1 with cervical cancer. METHODS: A total of 181 samples including 90 cervical cancer patients and 91 healthy controls were genotyped. The genotype frequencies of these polymorphisms in collected samples were determined by either PCR-RFLP or PCR-ARFLP methods...
April 1, 2018: International Journal of Biological Markers
Sinda A Bedoui, Mouadh Barbirou, Mouna Stayoussef, Meriem Dallel, Amina Mokrani, Lamia Makni, Amel Mezlini, Balkiss Bouhaouala, Besma Yacoubi-Loueslati, Wassim Y Almawi
BACKGROUND: Interleukin (IL)-17A is proinflammatory cytokine produced by Th17 cells, which play key, but sometimes inconsistent role in autoimmunity and cancer. Polymorphic variants in IL-17A gene were differentially associated with susceptibility to cancer, including colorectal cancer (CRC). AIM: We investigated the association between six IL-17A gene variants (rs3819024, rs2275913, rs3819025, rs10484879, rs7747909, and rs3748067) with CRC susceptibility in Tunisians...
April 21, 2018: Cytokine
Daniel Jablonski, Václav Gvoždík, Lukáš Choleva, David Jandzik, Jiří Moravec, Zdeněk Mačát, Milan Veselý
The maternal origin of isolated populations of the common wall lizard (Podracis muralis) in the Czech Republic, representing the north-eastern range border of the species, was addressed. We compared mitochondrial DNA sequences of the cytochrome b gene of samples from these populations with those from within the continuous range in Slovakia, the northern Balkan region, and those available from previous studies. We recorded five main haplogroups in the studied region, with all available Central European samples belonging to the same haplogroup...
April 21, 2018: Mitochondrion
Maxime Bastien, Chiheb Boudhrioua, Gabrielle Fortin, François Belzile
Genotyping-by-sequencing (GBS) potentially offers a cost-effective alternative for SNP discovery and genotyping. Here, we report the exploration of GBS in tetraploid potato. Both ApeKI and PstI/MspI enzymes were used for library preparation on eight diverse potato genotypes. ApeKI yielded more markers than PstI/MspI but provided a lower read coverage per marker, resulting in more missing data and limiting effective genotyping to the tetraploid mode. We then assessed the accuracy of these SNPs by comparison with SolCAP data (5,824 data points in diploid mode and 3,243 data points in tetraploid mode) and found the match rates between genotype calls was 90...
April 24, 2018: Genome Génome / Conseil National de Recherches Canada
Ludmila Volozonoka, Dmitry Perminov, Liene Korņejeva, Baiba Alkšere, Natālija Novikova, Evija Jokste Pīmane, Arita Blumberga, Inga Kempa, Anna Miskova, Linda Gailīte, Violeta Fodina
PURPOSE: To compare multiple displacement amplification and OmniPlex whole genome amplification technique performance during array comparative genome hybridization (aCGH), Sanger sequencing, SNaPshot and fragment size analysis downstream applications in frame of multifactor embryo preimplantation genetic testing. METHODS: Preclinical workup included linked short tandem repeat (STR) marker selection and primer design for loci of interest. It was followed by a family haplotyping, after which an in vitro fertilization preimplantation genetic testing (IVF-PGT) cycle was carried out...
April 23, 2018: Journal of Assisted Reproduction and Genetics
Mohamed Saleem, Mohd Bazli Ghazali, Md Azlan Mohamed Abdul Wahab, Narazah Mohd Yusoff, Hakimah Mahsin, Ch'ng Ewe Seng, Imran Abdul Khalid, Mohd Nor Gohar Rahman, Badrul Hisham Yahaya
Approximately 5-10% of breast cancers are attributable to genetic susceptibility. Mutations in the BRCA1 and BRCA2 genes are the best known genetic factors to date. The goal of this study was to determine the structure and distribution of haplotypes of the BRCA1 and BRCA2 genes in early-onset breast cancer patients. We enrolled 70 patients diagnosed with early-onset breast cancer. A total of 21 SNPs (11 on BRCA1 and 10 on BRCA2) and 1 dinucleotide deletion on BRCA1 were genotyped using nested allele-specific PCR methods...
April 24, 2018: Advances in Experimental Medicine and Biology
Marie Noelle Ndjiondjop, Kassa Semagn, Mounirou Sow, Baboucarr Manneh, Arnaud C Gouda, Sèdjro B Kpeki, Esther Pegalepo, Peterson Wambugu, Moussa Sié, Marilyn L Warburton
Using interspecific crosses involving Oryza glaberrima Steud. as donor and O. sativa L. as recurrent parents, rice breeders at the Africa Rice Center developed several 'New Rice for Africa (NERICA)' improved varieties. A smaller number of interspecific and intraspecific varieties have also been released as 'Advanced Rice for Africa (ARICA)'. The objective of the present study was to investigate the genetic variation, relatedness, and population structure of 330 widely used rice genotypes in Africa using DArTseq-based single nucleotide polymorphisms (SNPs)...
2018: Frontiers in Plant Science
Stuart Cantsilieris, Bradley J Nelson, John Huddleston, Carl Baker, Lana Harshman, Kelsi Penewit, Katherine M Munson, Melanie Sorensen, AnneMarie E Welch, Vy Dang, Felix Grassmann, Andrea J Richardson, Robyn H Guymer, Tina A Graves-Lindsay, Richard K Wilson, Bernhard H F Weber, Paul N Baird, Rando Allikmets, Evan E Eichler
Structural variation and single-nucleotide variation of the complement factor H ( CFH ) gene family underlie several complex genetic diseases, including age-related macular degeneration (AMD) and atypical hemolytic uremic syndrome (AHUS). To understand its diversity and evolution, we performed high-quality sequencing of this ∼360-kbp locus in six primate lineages, including multiple human haplotypes. Comparative sequence analyses reveal two distinct periods of gene duplication leading to the emergence of four CFH -related ( CFHR ) gene paralogs ( CFHR2 and CFHR4 ∼25-35 Mya and CFHR1 and CFHR3 ∼7-13 Mya)...
April 23, 2018: Proceedings of the National Academy of Sciences of the United States of America
J Xu, H Zhang, Y Gu, K Mehmood, Q Zhang, M Ijaz, R Z Abbas, W Babar, S Li
Cluster of differentiation 4 (CD4) is an important molecule in the immune system of animals, which participates in the processes of T-lymphocyte differentiation, maturation, immune response and signal transduction. During this study, we adopted the direct sequencing of PCR products and time-of-flight mass spectrometry methods for the detection of single nucleotide polymorphisms (SNPs) in 382 Yorkshire pigs. The linkage disequilibrium of CD4 gene polymorphisms and their genetic effects on blood routine indexes were also analyzed...
March 2018: Journal of Biological Regulators and Homeostatic Agents
Chen Peng, Ying Ding, Xin Yi, Zhiqiang Dong, Limei Cao, Qiang Li, Haiyan Ren, Lin He, Daizhan Zhou, Xu Chen
Aims Ischemic stroke (IS) is one of the most common diseases of neurology and the main cause of death and disability in Chinese population. CACNA1C was considered to be involved in the process of atherosclerosis, but there was little information about the association between genotypic polymorphisms of CACNA1C and ischemic stroke. Our study was designed to elucidate the relationship between four single-nucleotide polymorphisms (SNPs) variants in CACNA1C gene and the risk of large-artery atherosclerotic (LAA) stroke patients...
April 23, 2018: Neurological Research
Gustavo Mendonça André, Camila Martins Trevisan, Isabela Nacione Pedruzzi, Ramon Felix Martins Fernandes, Renato Oliveira, Denise Maria Christofolini, Bianca Bianco, Caio Parente Barbosa
Endometriosis is an estrogen-dependent inflammatory disease that affects a large number of women in reproductive age. Follicle-stimulating hormone (FSH) plays a role in steroidogenesis and acts through a transmembrane glycoprotein, FSH receptor (FSHR). Polymorphisms in FSHR gene were previously associated with variability in FSH serum level and reproductive outcomes, but its relation with endometriosis has not been clarified and demonstrated conflicting results, ranging from strong links to no association to endometriosis...
April 23, 2018: DNA and Cell Biology
Ramcés Falfán-Valencia, Arun Narayanankutty, Juan M Reséndiz-Hernández, Gloria Pérez-Rubio, Alejandra Ramírez-Venegas, Karol J Nava-Quiroz, Nora E Bautista-Félix, Gilberto Vargas-Alarcón, Manuel D J Castillejos-López, Andrés Hernández
Background: The influenza A H1N1/09 pandemic infected a small number of exposed individuals, which suggests the involvement of genetic factors. There are scarce data available on classical HLA class I association with the influenza A H1N1/09 pandemic. Methods: We analyzed the frequency of classical HLA class I alleles and haplotypes in A H1N1/09 influenza in a case-control study including 138 influenza patients (INF-P) and 225 asymptomatic healthy contacts (INF-C) simultaneously recruited...
2018: Journal of Immunology Research
Junxin Zhang, Moqi Yan, Yijian Zhang, Huilin Yang, Ye Sun
Developmental dysplasia of the hip (DDH) is a common skeletal disorder whereby genetic factors play a role in etiology. Multiple genes have been reported to be associated with the occurrence of DDH. WISP3 gene was found to be a causative gene for progressive pseudorheumatoid dysplasia (PPD). Reports of WISP3 gene in association with DDH are lacking. We conducted a case-control candidate gene association study enrolling three hundred and eighty-six patients with radiology confirmed DDH and 558 healthy controls...
April 19, 2018: Gene
Tunde I Huszar, Mark A Jobling, Jon H Wetton
Short tandem repeats on the male-specific region of the Y chromosome (Y-STRs) are permanently linked as haplotypes, and therefore Y-STR sequence diversity can be considered within the robust framework of a phylogeny of haplogroups defined by single nucleotide polymorphisms (SNPs). Here we use massively parallel sequencing (MPS) to analyse the 23 Y-STRs in Promega's prototype PowerSeq™ Auto/Mito/Y System kit (containing the markers of the PowerPlex® Y23 [PPY23] System) in a set of 100 diverse Y chromosomes whose phylogenetic relationships are known from previous megabase-scale resequencing...
April 12, 2018: Forensic Science International. Genetics
Opal Pitaksakulrat, Bonnie L Webster, Joanne P Webster, Thewarach Laha, Weerachai Saijuntha, Poppy H L Lamberton, Nadda Kiatsopit, Ross H Andrews, Trevor N Petney, Paiboon Sithithaworn
The liver fluke Opisthorchis viverrini sensu lato causes serious public-health problems in northeast Thailand and Southeast Asian countries. A hypothesis has been proposed that O. viverrini represents a species complex with varying levels of genetic differentiation in Thailand and Lao PDR. This study aimed to clarify whether O. viverrini populations can be genetically divided into separate taxa. We collected O. viverrini s.l. from eight different locations in Lao PDR and Thailand. The results of nad1, cox1, CF-int6, Pm-int9, ITS2 and 28S rDNA sequence analysis revealed that sub-structuring occurred between the eight populations...
April 18, 2018: Infection, Genetics and Evolution
Marta Podralska, Iwona Ziółkowska-Suchanek, Magdalena Żurawek, Agnieszka Dzikiewicz-Krawczyk, Ryszard Słomski, Jerzy Nowak, Agnieszka Stembalska, Karolina Pesz, Maria Mosor
BACKGROUND: DNA damage repair is a complex process, which can trigger the development of cancer if disturbed. In this study, we hypothesize a role of variants in the ATM, H2AFX and MRE11 genes in determining breast cancer (BC) susceptibility. METHODS: We examined the whole sequence of the ATM kinase domain and estimated the frequency of founder mutations in the ATM gene (c.5932G > T, c.6095G > A, and c.7630-2A > C) and single nucleotide polymorphisms (SNPs) in H2AFX (rs643788, rs8551, rs7759, and rs2509049) and MRE11 (rs1061956 and rs2155209) among 315 breast cancer patients and 515 controls...
April 20, 2018: BMC Cancer
Naser Kalantari, Nastaran Keshavarz Mohammadi, Pantea Izadi, Saeid Doaei, Maryam Gholamalizadeh, Hassan Eini-Zinab, Tuire Salonurmi, Shahram Rafieifar, Reza Janipoor, Ghasem Azizi Tabesh
BACKGROUND: Single-nucleotide polymorphisms (SNPs), which are located in the first intron of the FTO gene, are reported to be associated with body weight and the body mass index (BMI). However, their effects on anthropometric measurements in adolescents are poorly understood. OBJECTIVE: This study aimed to investigate the association of three adjacent polymorphisms (rs9930506, rs9930501, & rs9932754) in the FTO gene with anthropometric indices in Iranian adolescent males...
2018: PloS One
Phillip A Morin, Andrew D Foote, C Scott Baker, Brittany L Hancock-Hanser, Kristin Kaschner, Bruce R Mate, Sarah L Mesnick, Victoria L Pease, Patricia E Rosel, Alana Alexander
Mitochondrial DNA has been heavily utilized in phylogeography studies for several decades. However, underlying patterns of demography and phylogeography may be misrepresented due to coalescence stochasticity, selection, variation in mutation rates, and cultural hitchhiking (linkage of genetic variation to culturally transmitted traits affecting fitness). Cultural hitchhiking has been suggested as an explanation for low genetic diversity in species with strong social structures, counteracting even high mobility, abundance and limited barriers to dispersal...
April 19, 2018: Molecular Ecology
Feng Cui, Yanyan Yu, Fangyin Bao, Song Wang, Ming Song Xiao
The oriental river prawn (Macrobrachium nipponense) is an economically and nutritionally important species of decapod crustaceans in China. Genetic structure and demographic history of Macrobrachium nipponense were examined using sequence data from portions of the mitochondrial DNA cytochrome oxidase subunit I (COI) gene. Samples of 191 individuals were collected from 10 localities in the upper to middle reaches of the Huaihe River. Variability was detected at a total of 42 nucleotide sites along 684 bp length of homologous sequence (6...
April 19, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"